be a little clearer about relationship among workflows

internal-instructions.md

@@ -2,20 +2,25 @@
 <!-- DON'T EDIT THIS SECTION, INSTEAD RE-RUN doctoc TO UPDATE -->
 **Table of Contents**
 
+- [Available workflows](#available-workflows)
 - [Running `scpca-nf` as a Data Lab staff member](#running-scpca-nf-as-a-data-lab-staff-member)
   - [Additional flags and parameters](#additional-flags-and-parameters)
   - [Testing the workflow](#testing-the-workflow)
   - [Running `scpca-nf` for ScPCA Portal release](#running-scpca-nf-for-scpca-portal-release)
   - [Processing example data](#processing-example-data)
 - [Maintaining references for `scpca-nf`](#maintaining-references-for-scpca-nf)
   - [Adding additional organisms](#adding-additional-organisms)
-- [Adding additional cell type references](#adding-additional-cell-type-references)
+  - [Adding additional cell type references](#adding-additional-cell-type-references)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
+## Available workflows
 
 ## Running `scpca-nf` as a Data Lab staff member
 
+This section provides instructions for running the main workflow, found in [`main.nf`](main.nf).
+Note that there are two other workflows: [`build-index.nf`](build-index.nf) for building reference indices (see #adding-additional-organisms), and [`build-celltype-ref.nf`](build-cellltype-ref.nf) for creating cell type annotation references.
+
 The instructions below assume that you are a member of the Data Lab with access to AWS.
 Most of the workflow settings described are configured for the ALSF Childhood Cancer Data Lab computational infrastructure.
 To process samples that are not part of the ScPCA project, please see the [instructions on using `scpca-nf` with external data](external-data-instructions.md).
@@ -99,6 +104,7 @@ Make sure to adjust the settings to make the zip file publicly accessible.
 
 ## Maintaining references for `scpca-nf`
 
+
 Inside the `references` folder are files and scripts related to maintaining the reference files available for use with `scpca-nf`.
 
 1. `ref-metadata.tsv`: Each row of this TSV file corresponds to a reference that is available for mapping with `scpca-nf`.
@@ -124,6 +130,8 @@ This file is required as input to the `build-celltype-ref.nf` workflow, which wi
 
 ### Adding additional organisms
 
+Adding additional organisms is handled, in part, by the `build-index.nf` workflow.
+
 Follow the below steps to add support for additional references:
 
 1. Download the desired `fasta` and `gtf` files for the organism of choice from `Ensembl`.
@@ -144,7 +152,10 @@ homo_sapiens
 4. Generate the index files using `nextflow run build-index.nf -profile ccdl,batch` from the root directory of this repository.
 5. Ensure that the new reference files are public and in the correct location on S3 (`s3://scpca-references`).
 
-## Adding additional cell type references
+### Adding additional cell type references
+
+Adding additional organisms is handled, in part, by the `build-celltype-ref.nf` workflow.
+
 
 Follow the below steps to add support for additional cell type references.
 We currently only support `celldex` and `PanglaoDB` for reference sources for `SingleR` and `CellAssign` cell type annotation, respectively.